Mitochondrial fatty acid -oxidation is traditionally viewed as an energy-generating, catabolic pathway but intermediates of this pathway can serve as key substrates for synthesis of other complex lipids. The long range objective of this project is to define the role of fatty acid oxidaton proteins in intermediary metabolism and the clinical impact of their deficiency due to inborn errors. The goal of the first funding period was to characterize the functional roles of LCAD, VLCAD, and ACAD9 and to explore the ramifications of genetic deficiencies of these enzymes in humans and mouse models. Significant progress has been made on each of these aims. Our chief findings include the ground breaking identification and partial purification of a multifunctional fatty acid oxidation complex containing all of the activities of this pathway in association with the mitochondrial respiratory chain super complexes and identification of the first patient with LCAD deficiency, presenting as predicted with a surfactant deficiency. The goal of this renewal application is to examine the expanding role of long chain fatty acid oxidation in normal metabolism and disease. It has three specific aims. Specific Aim 1 is to characterize the structure of the multifunctional fatty acid oxidation complex and its interaction with the mitochondrial respiratory chain. I hypothesize that this contact is critical to the channeling of reducing equivalents from fatty acid oxidation to the respiratory chain and that disruption of this process reduces the efficiency of mitochondrial energy generation. Specific Aim 1a is to elucidate the mechanism of electron transfer by first deducing the structure of the multifunctional FAOD complex using cryoelectron microscopy. Specific Aim 1b is to examine the role of patient identified mutations on VLCAD function, including their effect on the integrity of the FAOD multifunctional complex. Specific Aim 1c is to characterize the integrity of the fatty acid oxidatin complex in VLCAD and LCAD deficient mouse models. Specific Aim 2 is to characterize the disparate effects of null and point mutations in the ACAD9 gene on protein structure and function. I hypothesize that ACAD9 serves a duel function in mitochondria as a metabolic enzyme and a respiratory chain assembly/stability factor. Specific Aim 2a is to examine the metabolic and moonlighting functions of ACAD9 in cells from deficient human patients. Specific Aim 2b is to characterize the range of biochemical and clinical effects in an ACAD9 knock out mouse model. Specific Aim 3 is to further characterize LCAD deficiency in patients and a knock out mouse model, and to elucidate its function in surfactant metabolism. Specific Aim 3a is to examine surfactant metabolism in wild type and LCAD deficient primary pneumocytes. Specific Aim 3b is to characterize the incidence and spectrum of clinical symptoms in LCAD deficiency.